Mass Effect: Rebirth
by ShepardCommander147
Summary: Set during the events of Mass Effect 2 After Shepard's untimely demise and unexpected revival Shepard is coerced to work with his temporary ally The Illusive Man to find the reason for the brutal attacks on human colonies. [Work in progress] Cover credit: Screenshot by johntesh on deviantart
1. 1: A Hero's Demise

**Rebirth Chapter 1: A Hero's Demise**

"Commander on deck!" a marine shouted as Shepard stepped into the CIC from the stairwell.

Shepard made his way to his station in the center of the CIC where Presley stood at attention in front of him. Presley's skin was slightly tanned, and he kept a well-trimmed beard and mustache, his eyes were blue and shimmered ever so slightly under the Normandy's lighting, "Status report?" Shepard asked as he surveyed the navigational data present in the center console.

"We're on course and proceeding on our patrol route, we'll be nearing the gravity well of a large planetoid shortly," Presley said stepping down from the command post and pausing to take a breath. "Nothing out of the ordinary, so far scans have been all but quiet, except for the occasional background radiation."

Shepard gave Presley a respectful nod in acknowledgment and stepped up to the command post. He watched as Presley assumed his secondary station to his left and quickly went back to work. John let out a sigh of relief as he tapped the center console causing his omni-tool to synchronize with ship systems, "Commander Shepard has command, XO Presley stands relieved," the Normandy's VI announced.

Shepard glanced at the display of his terminal, which was now showing the sensor readouts of the system. Nothing, yet countless ships had gone missing in this sector, but nothing seemed amiss, "Could be pirates," he thought as he tapped the screen to open an array of different menus, "but why would they hit this system in particular?"

"Commander," Presley said breaking John from his thoughts, "we're picking up a signature on sensors nearby, it's massive."

"Geth?" John asked as he pulled up the signature on his displays.

"It doesn't match any ship profile we know of, I don't think it's Geth, but I can't tell for sure."

"Keep us running silent and notify me if it does anything out of the ordinary."

"Will do Commander."

It'd only been a few minutes before Presley broke John's train of thought again, "Commander," he said turning to get John's attention, "the ship is on an intercept course."

That'd been enough to kick himself into gear as his muscles tensed and his mind began to run through various scenarios in his head, "Take evasive action," John said as his crew complied to his command within seconds like the well-oiled machine they were.

"They're adjusting to match sir," Presley said.

John pounded a clenched fist onto the terminal, "Bring weapons online and issue condition red," he said. A few seconds later and the lights around them were blinking red, and he could hear the sound of crewmen running down the walkways taking their stations and strapping themselves in as the Normandy's VI stated the obvious in case the blinking lights hadn't conveyed the message, they were under attack.

Shepard looked down on his console which was displaying a tactical readout showing the Normandy and the incoming vessel which the combat VI had named red one, "Lock weapons on red one," John said

"Weapons locked," His gunnery officer Addison replied.

"Open a channel to the enemy ship and transmit," John said

"Channel open," Presley said.

"Unidentified vessel this is Commander John Shepard of the S.S.V Normandy break your intercept course, or you will be fired upon," he said before tapping his display slightly which ended the transmission.

Moments later he was launched off his feet as a blast collided with the Normandy's hull plating

"Returning fire!" Addison yelled as the deafening screech of the Normandy's GUARDIAN lasers fired in unison on their attacker.

John grasped at the railing in front of him and pulled himself up, though he was instantly flung back again as another beam hit them. The consoles around him surged blasting arcs of electricity haphazardly while conduits of fluid and gas burst from the walls and deck plating below. He turned to see Presley lying a few feet away his eyes open staring blankly forward; his blue eyes seemed to lose their shimmer as the white lights faded, replaced by the red luminesce of the emergency lighting, "Presley is down someone get me a medic!" Shepard yelled as he crawled over to Presley. "Joker get us out of here!" John yelled though his words were cut off by the deafening screech of metal being torn apart, like nails on a chalkboard.

"I'm trying to lose them!" Joker said as his voice crackled through the intercom next to him.

John looked back to see a marine, Private Fredricks if he recalled correctly, rushing to Presley's aid. Fredricks was only a few feet away from them and was using the railing by the gunnery terminals for support as he closed in on their position. Suddenly a conduit ruptured near the marine spewing out a liquid he couldn't recognize though before he could react the spark from the console set the once harmless substance alight. John rushed over to the man now seizing on the floor beside him. The fluid had already burned out almost as quickly as it had ignited though it left the Marine's face mangled and torn. The once smooth skin now torn and charred as his pores oozed liquid and his left eyelid looked as if it had melted shut, "Private can you hear me?" John said as he knelt over the man.

"Y-Yes Commander," the Private murmured as though he was pouring every ounce of will power he had just to push the words out of his throat.

"Stay with me Fredricks, that's an order!" Shepard said as he gripped the marines hand in his and squeezed. "Someone get me a fucking medic over here!" he yelled. John turned back to the young Private as the marine's grasp loosened, "Don't you fucking die on me, you hear me? Private, answer me!" John repeated.

It felt like hours had passed he was still kneeling over the marine's body, holding his lifeless hand tightly. The sensation of someone pulling on his shoulder brought him back to reality as he turned to see Liara her dark blue skin glistening with sweat and dotted with dark spots of ash, "Shepard we have to evacuate!" she said handing him his helmet.

John slid the mask over his head as the helmet sealed around him, though without the proper equipment it wouldn't keep him alive if happened to run into a hull breach, "Damn it," he whispered under his breath.

"Do you know where Joker is? He wasn't in any of the escape pods I checked!" Liara yelled to make herself heard over the hissing of sparks and grinding of malfunctioning equipment.

A few seconds went by as he tried to push all the emotions out of his head, "He's in the cockpit, get to the escape pod, I'll get him!" he said.

Liara gave him a squeeze in the arm, "Don't do anything stupid John," she said, "and keep an open channel."

John nodded as he tapped the small transmitter on the side of his helmet, ensuring they were on the same frequency and headed toward the cockpit.

A minute later and he'd came to the end of the small corridor where large sections of the hull were replaced with emergency mass effect fields to prevent losing atmosphere, "Joker!" he cried out to get his pilot's attention.

"I'm not leaving Commander; I'll be damned before I leave the Normandy to die at the hands of these bastards!" Joker yelled back, his voice muffled by the emergency rebreather he was wearing which obscured his voice slightly, while whatever pathetic armaments the Normandy had left fired on their attacker once more.

"Joker the Normandy's lost, don't throw your life away!"

Joker turned to face him, his eyes glaring with determination, "I've already launched our distress beacon Commander, I'll lure this bastard away from here."

"Like hell you will!" Shepard said as he slammed the panel connected to the escape pod that was on the left wall next to them. John grabbed Joker by the arm and yanked his seat restraints off, he'd probably broken Joker's arm, but he'd thank him later. With a forceful pull, he shoved Joker into the pod though before he could follow another beam of energy sheared through the cockpit. John slammed the panel, sealing the pod as Joker banged against the door trying to find the override. Shepard called upon whatever strength he had left as he slapped the panel one last time, launching the pod.

"I love you Liara," he said as he tried his best to form what little breath he had left into coherent words. He let go of the railing he was holding onto as he was pulled into the black void of space which was littered with pieces of what used to be his ship, his home.

"John what's happening! Can you hear me?" Liara asked frantically

John tried to respond, but he could only gasp for breath that would never come. He tried to fight the burning pressure inside him as his lungs demanded air. John could still hear someone trying to get his attention through the transmitter in his helmet, but couldn't make out the words they were saying. He was trying to figure a way out of this though his planning was cut short when he felt a sharp pain at the back of his head as something smacked against his helmet, knocking him into unconsciousness as his eyes closed for the last time.

...

Liara stood in front of the crowded street in front of the Alliance headquarters on Earth; she could hear the chatter of pedestrians and the traffic of sky cars whizzing past above. The smell of flowers which only brought back the memories of her first date with John, he'd given some to her as part of a human custom. She felt a tear roll down her face causing her to pull her arm up and wipe it away discreetly. It'd been months since the destruction of the Normandy, and she still found herself mourning.

"Hard to believe he's really gone," Garrus said as he put a hand on her shoulder, "I didn't think anything could kill that stubborn bastard." Garrus shifted uncomfortably beside her obviously trying to cope with his usual sense of humor.

A few hours later and Liara was sitting on one of the reserved stages to the side of the center stage which had a podium, likely for those who wished to say their final good-byes. All of the Normandy's crew were present, and all of them had declined to speak. "What more was there to say?" she thought as she looked around the stage. She was on the end of the platform with Garrus sitting opposite of her and Wrex beside him. Joker was sitting at the far end of the stage; he hadn't spoken to her or anyone really ever since the attack, "Who could blame him?" she thought.

She could see Admiral Hackett with Captain Anderson, "Admiral Anderson now actually," she reminded herself. Anderson was sitting behind Hackett with another Alliance official she hadn't recognized. Though to her surprise, all members of the Council were present sitting to the far side of Hackett and Anderson with what looked like two Asari Commandos standing guard beside them dressed in full combat gear. "Thank you all for coming," Admiral Hackett said speaking into the podium at the front of the stage, "I wish we were gathered here under better circumstances." Liara shifted uncomfortably in her seat as Hackett continued, "We're here to mourn the death of one of humanities greatest hero's, Commander John Shepard, recipient of the Star of Tera, the hero of the Citadel, and the only damn reason Elysium is still standing." Small cheers erupted from the crowd as he continued. "Let humanity never forget the sacrifices he made in the battle against the Reapers," he said as some of the Council shifted uncomfortably, Udina included.

"Spineless vorcha," Wrex muttered to the amusement of the Normandy crew. The council had fought the idea of a Reaper threat hard and ever since the Normandy's destruction they'd fought even harder to undermine everything Shepard had fought for.

"John was right," Liara thought, "politicians did have a short memory when it suited them." Though now Hackett had said his peace and now Anderson was taking the stand. She could see the lines on his face they portrayed only grief, the pain of a father losing his son. She knew Anderson wasn't his real father but he was the closest thing Shepard had to a father, and Shepard was the closest thing Anderson had to a son.

"I'm not one for speeches," Anderson said softly, "no amount of words will bring John back but what we can do is carry on, like humanity always has. God-speed Commander." Anderson finished as he sat back down his hands covering his face.

Liara watched as Normandy's marines escorted John's casket down the street, normally this was done by honor guard, but Lieutenant Alenko had requested otherwise. The Marines marched behind Kaidan who was now leading his Marines towards the Commander's final resting place. Though not publicly known, the casket was empty. The Commander's body had been recovered but somehow to the Alliance's embracement, gone missing. Military fighters flew in formation above as the marine escort reached their destination and lowered the casket into the ground. A tear rolled down her cheek, and she let her head sag as she buried her face in her hands, "What were you expecting?" She thought, "For all of this to just go away from one little parade?"

Garrus put a warm hand on her back, "I miss him too," he said as he pulled her close.

...

A few months later Liara was sitting at her desk in her apartment on Illium; she'd been inquiring as to where Shepard's body had gone. "It wasn't right," she thought "his body isn't some trophy to be hoarded by some criminal." Liara shuddered at the thought of his body being preserved in some wealthy collector's home or even worse by some band of criminals. A ping from her terminal tore her from her thoughts, prompting her to open the message.

 _As per your request multiple broker agents have been interrogated and disposed of, our report will be attached to this message. I hope you find what you're looking for._

 _Captain Kirrahe_

Liara took a breath as she read the report and it'd only confirmed her suspicions. The broker had somehow stolen Shepard's body and if the Kirrahe's report was accurate, which she knew it was, were going to make a deal with the Collectors on Omega, "I thought the Collectors were a myth," she thought as she closed the report. Omega was still a bit of a blind-spot in her small intelligence network she'd formed in her search for Shepard's body, "Thankfully I know just the Turian for the job," she thought grinning to herself as she began her message to Garrus.

Garrus had made a bit of a name for himself on Omega, without Shepard most of the Normandy crew had gone their separate ways. Garrus had taken to becoming a vigilante of sort on Omega, "Leave it to Garrus," she thought, "righting the galaxies wrongs one at a time." She stood up from her desk, still pondering how to approach the message, "This my wrong to right," she thought, "knowing Garrus he'll insist on handling it himself." She thought as she poured herself a cup of coffee and a few minutes later the encrypted message was on its way to Omega, and she would soon follow.

 _Thanks for reading Chapter 1 of Rebirth, there will be more to come soon as I will be adding chapters once I finish and review them. Please leave a review if you feel like it, constructive criticism is always encouraged._


	2. 2: Resurgence

**Chapter 2: Resurgence**

John woke to the pulsing sounds of alarms and the noxious smell of smoke and burning coolant, "Shepard!" a female voice shouted at him through the intercom with a slight Australian accent. "Commander you need to get up, we-we're under attack!" the woman said, as gunshots rang out nearly overshadowing her voice.

Shepard pondered on the words for a moment, his mind still clouded from, "Where the hell am I?" he thought as his memories came flooding back to him. The clanking of metal broke him from his thoughts as he turned to see a slim security mech holding a pistol approaching him. His training quickly took over as he rolled into cover by the narrow metal door frame where the droid was approaching from. He mustered up what little energy he had left into a mass effect field as he leaped in front of the doorway, releasing the biotic energy at the droid, knocking it off balance. He quickly put the droid in a headlock and squeezed as hard as he could against the metal frame, a few seconds later his efforts were rewarded with a loud crack as the head tore from the frame. Sparks burst onto his arm, scorching the flesh, "Damn it!" he cursed, throwing the droid on the ground.

"Shepard? Are you all right?" the woman asked.

"Who was this woman and should he trust her?" he thought to himself as he picked up the security mech's pistol from its motionless frame. "Yeah, I'm fine," John said, "who the hell are you, and where are we?" he asked.

"Listen," the women said sternly, "I don't have time to explain, all you need to know is the station is under attack, and I'm one of the few things on this station that isn't trying to kill you." More gunfire interrupted her briefly before she continued, obviously winded from the ordeal, "Make your way to docking bay three, we have a shuttle waiting for you."

John waited a few seconds, contemplating his response before finally breaking the uneasy silence, "I'll be there," as he made his way down the hallway at a brisk pace, pistol in hand.

It'd only been a few minutes of running before the sounds of gunfire slowed his pace to a low crouch as he turned the corner. John could see a small room with various tech equipment lying about and what looked to be server equipment, "Some kind of server hub?" he thought as he turned examined the source of the gunfire. Three security mechs were closing in on a man who was taking shelter behind a console, the man was trying to do interface with the terminal, he stopped when he saw Shepard around the corner.

"Help! These mechs have gone crazy, please!" the man said as quickly ducked behind the terminal.

John fired his pistol at one of the mechs, the shot only grazing its shoulder. The mech quickly turned around to face him, he immediately fired another shot into the head of the mech. This shot had hit its mark as the droid crumpled to the ground, though the victory was short lived as a shot grazed his shoulder. "Fuck!" John shouted as he was forced back to cover. He quickly surveyed the wound, it was bleeding, but it wasn't going to be serious, not for a few hours anyway. The sound of another gunshot bolted him out from cover, he fired a volley of bullets into the first droid which was now facing the man at the other end of the room. The other turned to face him, he quickly mustered another weak biotic-field and released it at the other droid and fired his pistol. The droid shot, though the biotic push had thankfully caused the bullets to miss their intended target, and instead lodge into the doorframe above him with a loud clang.

"Shit!" the man in the corner yelled as he limped around the terminal, "they hit me in the fucking leg!"

"Yeah, get in line," John said as he yanked the man towards him. He wasn't very impressive up close, the man had pasty white skin and slim build and a tight jumpsuit, "Probably a technician," he thought to himself as they headed out the doorway.

"Slow down!" The technician said frantically a few feet behind John.

John reluctantly complied as they turned around another corridor, though they seemed to be getting close to the hangar, "What were you doing in there?" he asked.

A few moments had passed before the technician replied, "Backing up data."

"I didn't get your name either," John said.

"Wilson," the technician replied.

John nodded slightly in acknowledgment as he entered a wide open room where a dark skinned man was kneeling in cover, the man had short black hair and a what looked to be light combat gear. A barrage of fire sent John diving for the cover next to the man as he heard the clumsy thud of Wilson following behind him.

"Shepard?" The man beside him asked, "Damn if Miranda has you up…"

"Nice to meet you too," John said as he peeked out slightly from cover. "Looks like four mechs on the catwalk, two on each sided trying to set up a crossfire, standard mech tactics."

"Sorry," the man said, "names Jacob, I'm Miranda's second, and I run security."

"It always this exciting?" John asked as he launched a biotic-field, lifting two of the drones helplessly flailing in the air.

"Not usually," Jacob said, letting a small grin escape as he fired on the two floating droids with his SMG, shredding the mechs into pieces.

"Where are we exactly? Miranda wasn't exactly able to give me the grand tour," John said, laying down cover fire.

"You're on a Cerberus research station," Jacob said as he ejected a thermal casing from his gun, causing searing hot air to erupt from the side of his weapon.

John's muscles tensed slightly as the air brushed against his face, "What the hell had he gotten himself into?" he thought as he surveyed Jacob, the golden emblem of Cerberus on the front of his uniform. He silently cursed himself.

"I guess Miranda left that part out…" Jacob muttered

John could see Jacob's muscles tense as they both stared each other down, "Listen," Jacob continued, "We can explain this later but right now we need to get to the hangar bay, Cerberus isn't what you think it is Commander."

John paused for a moment, his muscles still tensed and weapon pointed towards the Cerberus agent, though still well aware of the technician cowering behind him. "He didn't kill me when he had the chance." John thought though the crack of a bullet hitting the railing drew his focus away. "They obviously want me alive, that's more than I can say for these drones," he thought as he lowered his pistol and nodded his head at Jacob, "You better have a damn explanation when this is over," he said.

"Cerberus isn't what you think it is Commander," Jacob said as he fired another volley of bullets at the remaining mechs sending them to the ground seizing as motors and pistons tried to compensate for the sudden force and missing extremities. "I was in the Alliance just like you, I know the stories and I was skeptical at first, but Cerberus isn't afraid to do what needs to be done. What the Alliance won't do."

"Like experimenting on kids and sabotaging freighters?" John said as he stood up from the railing which was now scorched and dented from the previous altercation.

"I know Cerberus has a colored past but we- we aren't like that. Not anymore. I wouldn't be here if I thought Cerberus were still doing that shit," Jacob said as he paused as if trying to see how he would react.

John simply nodded as Wilson interrupted, "Let's get out of here, this station's falling apart!"

"You grab any meds on your way out Doc?" Jacob asked.

"Doc?" John asked as they continued down the corridor

"What's a Doctor doing backing up data in a server room, several decks above the medical bay?" John asked as they turned the corridor.

A shot sent John diving for cover as he pointed his gun toward the source, "My thoughts exactly," the woman said, the same voice he'd heard in the med-bay.

"What the hell Miranda!" Jacob said as he looked down at Wilson's corpse.

"He's the one who turned the mechs on us Jacob," Miranda said as she holstered her pistol. "I always knew he had his doubts about the… ethics of our work, I just didn't think he'd be foolish enough to act on them."

John got up slowly from the floor, studying the woman in front of him. She had black hair and light blue eyes, her uniform was white in the center with the shoulders and arms colored black. Her body type was slim, and she carried a holster on her belt, "I want some answers!" he said as he faced the woman.

"Of course, we can explain it on the way. Unless of course, you'd rather stay here with the mechs," she said as she opened the door to the hangar.

 **-()-**

A few hours later and John found himself staring down the hologram of The Illusive Man himself. He wore a dark black suit and held a cigarette in his hand which left a lingering trail of smoke in its path as he brought it to his mouth and back down. "Commander Shepard," The Illusive Man said as he brought his cigarette down to the side of his chair, the mere sound of his voice seemed to command respect.

"Illusive man," John said plainly as observed the dark room around him, it was small and circular with only the projection to provide light.

"Do you know why you're here?" he said.

"Are you going to give me some speech about the _noble_ goals of Cerberus if I ask?"

"You died, Shepard."

As if someone had put the pieces back together, it all surged back to him, "What did you do to my ship! Where the hell is my crew!"

"Your crew is fine," he said taking a sip from the small cup he held in his other hand. "You, on the contrary, died two years ago."

"Then why'd you bring me back? What do you gain out of all this?"

The Illusive Man let a smile escape as if he'd been waiting to play his hand, "Humanity is under attack, entire colonies have gone missing."

"Then why did you spend would you spend all this time bringing me back? You could've hired a small army for the trillions you spent bringing me back."

"Humanity doesn't need an army, they need a symbol, a leader… hope."

"John looked the man in the eye, "I'll investigate these attacks but that's it, but if you're lying to me…"

"Threats won't be necessary Commander, I assure you, my information is accurate," The Illusive Man said, the hint of a smile creeping across his face.

"Where do I start?" John said.

The Illusive Man paused for a moment as he finished the last of his drink and set it down with a soft clink resonating slightly through the call, "We've lost contact with a colony, Freedoms Progress, and if this is an attack…"

"I'll need a ride," John said.

"Of course, your shuttle is already prepped and waiting. Good luck, Commander," The Illusive Man said as he brought the cigarette to his mouth one last time as the projection faded to black.

John turned toward the door and headed to the shuttle bay he'd came from, as much as he hated Cerberus this was too important to pass up.

Miranda and Jacob were waiting for him by the shuttle along with what looked to be their pilot, "Great..." John said under his breath as he stepped inside the shuttle.

 **-()-**

John stepped out of the shuttle onto the white pavement below, Cerberus had provided him with an M-8 Avenger and an M-3 Predator, the Predator was clamped onto the side of the basic black hard-suit he'd been given, "Search for survivors," he said as he observed the multiple buildings around him.

"The mission comes first," Miranda said as she stepped out of the shuttle with Jacob following close behind.

" _Survivors,_ " he said turning to meet Miranda's gaze, "can tell us what happened here." John approached the entrance to one of the buildings, it was a simple residential prefab with two floors and a balcony that attached to catwalks leading to the other various buildings in the colony.

Shepard waved his hand over the panel revealing a large open room which was furnished with a small couch and a dining table with various other appliances sitting on the counter to their right which was likely the kitchen. "No sign of a struggle," John thought as he examined the nearly immaculate room, except for the occasional cup or datapad sitting on a table.

"It's like they just vanished," Jacob said as they made their way inside.

"Very odd it's al-," Miranda's words cut off by the sound of gunfire.

The first shot hit John's kinetic barriers, giving him just enough time to leap behind the nearby counter before the barrage of gunfire could break through his shields. He quickly popped up from cover firing a few shots blindly at the shooter which he could now make out to be a security mech, the same kind he'd fought previously though with slight alterations. He dropped back into cover before he could see if any of his shots had connected, though the sound of returning gunfire quickly answered that question.

"Got the bastard!" Jacob said as the mech hit the floor with a distinct clang.

Fifteen minutes later and they still hadn't found any survivors or any corpses for that matter, only the occasional rogue security mech.

"These mechs should've recognized us as humans," Miranda said as they approached the entrance to another prefab.

Shepard opened the door expecting to find another empty room though instead of bare furniture and empty space he was now looking at four heavily armed quarians. Each group readied their weapons at each other, a finely-honed instinct of training, "We aren't looking for trouble," John said staring down the sights of his Avenger.

"Shepard?" one of the quarians said, she was wearing an armored environmental suit with a purple hood over her head.

"Tali?" John said.

"I- I thought you were dead Shepard," Tali said now lowering her weapon.

John lowered his Avenger as he signaled for his team to do the same, "It didn't take," he said as his squad reluctantly lowered their weapons.

"What are you doing here?" Tali asked as she clamped the shotgun onto the back of her hard-suit. "And why are you with _Cerberus_ ," she said pointing accusingly to his two companions, each dawning Cerberus uniforms.

"What are quarians doing at a human colony?" Miranda said.

"I don't care who this guy is, we don't take orders from Cerberus!" one of the marines said brandishing his weapon.

"I'm sure he has his reasons, right Shepard?" Tali said

"It's a long story, but I _don't_ work for them," John said as he clamped the Avenger onto his back, "but what are a bunch of quarians doing at a human colony?"

"Veetor," Tali said, "he was on pilgrimage here, trying to barter for parts most likely. We lost contact with the colony and came to investigate."

"Awful _fast_ response time," Miranda said.

Tali ignored the comment, "Look, we think Veetor is in the main security building at the center of the colony, not too far from here."

"Sounds about right, that's the only area we haven't searched," John said.

"One problem though…" Tali said as she beckoned them to follow, "Veetor's reprogrammed one of the heavy mechs, it's guarding the building," she finished as they stepped outside.

"Great… more mechs," John said sighing.

Ten minutes later and John found himself pinned between a shipping crate and a very large mech, "I really fucking hate mechs," he said as he fired more rounds into the mech's shields. The sound of three thuds in rapid succession sent John into a low cover as he heard the whizz of the mech's missiles, "Get down!" He yelled into the com as the shockwave shook the crates he was crouching behind.

"My men are down!" Tali said into the com.

John heard the zap of Miranda's omni-tool as she overloaded the rest of the mech's shields with low powered, highly concentrated EMP, the rest of them followed up as the ringing sounds of gunfire followed by the shearing of metal and circuitry. The deafening sound of a chain-gun brought John back into cover, as volleys of bullets tore through the crate he was hiding behind, a few of the bullets breaking through his shields and lodging themselves into his shoulder and armor plating. "Get down," he heard Jacob yell through the com as a set of explosions sent shockwaves through the battered shipping crates.

"Good job," John said as he rolled out from cover to the sight of the crumpled mech.

"Let's get to Veetor," Tali said into the com as John got himself up slowly as he broke a small canister of medi-gel open and applied it to the exposed sections of his hard-suit that'd been torn open by the barrage of fire he'd taken.

"Monsters coming back," John could hear the quarian frantically murmuring to himself as they entered, "Mechs will protect, have to hide. No swarms no, no, no."

"Veetor?" John said as he approached the frantic quarian who was sitting at the back of the room.

"No Veetor, not here, swarms can't find."

"I don't think he can hear you, Commander," Jacob said as he stepped up beside Shepard.

"Veetor," John said as he put a hand on the quarian, "the swarms are gone."

Veetor looked up at Shepard, "You're human? How did you hide from the swarms?"

"We weren't here during the attack; can you show us what happened?" Shepard asked as he heard Tali step inside.

"Yes, yes," Veetor said as he interfaced with the console in front of him, his hands shaking as they glided over each interface.

The screen switched to blurry security footage with what appeared to be swarms of some sort of insect he couldn't recognize, "What the hell are those?" He thought as the footage panned over to reveal an insect-like humanoid, it had a broad head with two large eyes on each end of the head.

"Collectors," Miranda said.

"I thought Collectors were just a Myth?" Tali said

"They hardly ever deal in person," Miranda said as the footage continued on showing the insects loading colonists into some sort of container that John couldn't recognize, "they usually deal through some kind of middle man, pirates or slavers. Cerberus intel on them is… extremely limited."

"I've heard stories of young quarians trying to trade tech with the collectors for their pilgrimage, most either don't make it back or give up. I'd always thought they just ran into pirates but this…" Tali said as the footage carried on and then stopped abruptly, "Keelah…"

"We should bring Veetor with us," Miranda said turning to face Shepard, "we can give him medical treatment, maybe he can-"

"No," Tali interrupted, "I'm taking him back to the fleet, I'll give you a copy of his omni-tool data, but that's it."

"Of course," John said as he stepped aside to let Tali grab Veetor.

"Commander-," Miranda said.

"He goes with his people," Shepard said as he turned back to Tali.

"I'm glad to see you're still in charge," Tali said as she helped Veetor up.

"Call the shuttle," John said as he stepped outside. The cold air brushed against his face as he observed the deserted colony, "What have you gotten yourself into?" he thought as he rubbed his forehead as the rumble of an approaching shuttle broke him from his thoughts.

 **-()-**

"Your findings at Freedom's Progress are troubling…" The Illusive Man said as he brought his cigarette to his mouth, pausing to take a breath, "Though this only confirms my suspicions, these attacks are more than mere pirate raids." The Illusive Man continued as he set his cigarette down in a small tray on his seat, "They _need_ to be stopped."

"I'm going to need an army or a really good team," John said crossing his arms.

"I have a few ideas," The Illusive Man said as various dossiers projected around the room.

"Save it," John said, "I already have a team."

"Your team has gone their separate ways, and some of them I can't even track down." The Illusive Man said as the dossiers disappeared around him, "But this is your team Shepard, though I think you'll agree that substitutions will be required."

"You don't expect me to work from a shuttle, do you?" John said

"Of course not," The Illusive Man said as he tapped a console on his chair, ending the call.

"Shepard?" a familiar voice asked from behind.

"Joker!" John said as he turned to face the main, still wearing his tattered SR-1 cap.

"Commander you're going to like this, they only told me about this last night," Joker said as they approached one of the hangar bays.

John's eyes widened as the hangar door opened to reveal a sleek black and white ship sitting, the lights of the hangar reflecting off the slick armor plating, the words _Normandy_ painted on the side, "It's massive," he said.

"Double the size of the original," Joker said as they approached the loading ramp.

"Commander Shepard is on deck," the Normandy's VI stated as they stepped out of the airlock and into the CIC.

"God," Joker said as he let out a sigh, "It's good to hear that again."

John gave him a puzzled look as they stepped towards the center console.

"Ever since you…" Joker paused, "Everything went to shit without you Commander, we were your team, and the Alliance didn't really like that your team was comprised of a bunch of aliens. Everyone went their separate ways."

"Greetings Shepard," a synthetic female voice said as a blue orb projected from the center console.

"And there's the only downside," Joker said.

"A VI?" John asked.

"No," the orb said, "I am EDI, I control the ships cyberwarfare suits, and I provide tactical analysis."

"An AI," Shepard thought, "could be useful."

"You're not going to jettison us all out the airlock when we get underway, right?" John said.

"No," EDI said, "I am incapable of directly controlling ship functions besides my allotted systems."

John gave a small nod toward EDI and headed towards his new quarters, he had a lot of dossiers to review, "Prep the ship for launch once the crew is aboard, I want us underway within the hour."

"Destination?" Joker said.

"Omega," Shepard said recalling one of the dossiers that he thought might actually be useful, a scientist, Mordin Solus to be exact.

 _Thanks for reading Chapter 2 I had to make several changes to this and I sat on it for a few days, I couldn't quite get Freedom's Progress right in my eyes as it's hard to build character on two people Shepard doesn't trust but I have some ideas in the works especially with add more of the crew and maybe some original characters._

 _As always please leave a review it helps to get an outside perspective on what I'm doing right and what I'm doing wrong._

 _Edit: Sorry I had to add my scene transition markers again because for some reason they aren't getting copied over from Word._


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